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Changes to be committed:

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modified:   .gitignore
	new file:   pkg/obitax/default_taxonomy.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonnode.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obifind/iterator.go
	modified:   pkg/obitools/obifind/options.go
This commit is contained in:
Eric Coissac
2024-11-16 10:01:49 +01:00
parent f3d8707c08
commit 36327c79c8
9 changed files with 153 additions and 87 deletions
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33
pkg/obitools/obifind/iterator.go
View File

@@ -1,7 +1,6 @@
package obifind
import (
"bytes"
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -22,11 +21,7 @@ func IFilterRankRestriction() func(*obitax.ITaxon) *obitax.ITaxon {
}
func ITaxonNameMatcher() (func(string) *obitax.ITaxon, error) {
taxonomy, err := CLILoadSelectedTaxonomy()
if err != nil {
return nil, err
}
taxonomy := obitax.DefaultTaxonomy()
fun := func(name string) *obitax.ITaxon {
return taxonomy.IFilterOnName(name, __fixed_pattern__)
@@ -53,27 +48,25 @@ func ITaxonRestrictions() (func(*obitax.ITaxon) *obitax.ITaxon, error) {
}
func TaxonAsString(taxon *obitax.Taxon, pattern string) string {
text := taxon.ScientificName()
// var text string
// if __with_path__ {
// var bf bytes.Buffer
// path := taxon.Path()
if __with_path__ {
var bf bytes.Buffer
path := taxon.Path()
// bf.WriteString(path.Get(path.Len() - 1).ScientificName())
bf.WriteString(path.Get(path.Len() - 1).ScientificName())
// for i := path.Len() - 2; i >= 0; i-- {
// fmt.Fprintf(&bf, ":%s", path.Get(i).ScientificName())
// }
for i := path.Len() - 2; i >= 0; i-- {
fmt.Fprintf(&bf, ":%s", path.Get(i).ScientificName())
}
// text = bf.String()
// }
text = bf.String()
}
return fmt.Sprintf("%-20s | %10s | %10s | %-20s | %s",
return fmt.Sprintf("%-20s | %10s | %10s | %-20s",
pattern,
taxon.String(),
taxon.Parent().String(),
taxon.Rank(),
text)
taxon.Rank())
}
func TaxonWriter(itaxa *obitax.ITaxon, pattern string) {

69
pkg/obitools/obifind/options.go
View File

@@ -1,17 +1,14 @@
package obifind
import (
"errors"
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"github.com/DavidGamba/go-getoptions"
)
var __taxdump__ = ""
var __alternative_name__ = false
var __rank_list__ = false
var __selected_taxonomy__ = (*obitax.Taxonomy)(nil)
var __taxonomical_restriction__ = make([]string, 0)
var __fixed_pattern__ = false
@@ -20,24 +17,6 @@ var __taxid_path__ = "NA"
var __taxid_sons__ = "NA"
var __restrict_rank__ = ""
func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bool) {
if required {
options.StringVar(&__taxdump__, "taxdump", "",
options.Alias("t"),
options.Required(),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
} else {
options.StringVar(&__taxdump__, "taxdump", "",
options.Alias("t"),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
}
if alternatiive {
options.BoolVar(&__alternative_name__, "alternative-names", false,
options.Alias("a"),
options.Description("Enable the search on all alternative names and not only scientific names."))
}
}
func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__rank_list__, "rank-list", false,
options.Alias("l"),
@@ -48,31 +27,23 @@ func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
options.Description("Restrict output to some subclades."))
}
func CLISelectedNCBITaxDump() string {
return __taxdump__
}
func CLIHasSelectedTaxonomy() bool {
return __taxdump__ != ""
}
func CLIAreAlternativeNamesSelected() bool {
return __alternative_name__
}
func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
taxonomy, err := CLILoadSelectedTaxonomy()
taxonomy := obitax.DefaultTaxonomy()
if err != nil {
return nil, err
if taxonomy == nil {
return nil, fmt.Errorf("no taxonomy loaded")
}
ts := taxonomy.NewTaxonSet()
for _, taxid := range __taxonomical_restriction__ {
tx := taxonomy.Taxon(taxid)
if err != nil {
return nil, err
if tx == nil {
return nil, fmt.Errorf(
"cannot find taxon %s in taxonomy %s",
taxid,
taxonomy.Name(),
)
}
ts.InsertTaxon(tx)
@@ -81,24 +52,8 @@ func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
return ts, nil
}
func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
if CLISelectedNCBITaxDump() != "" {
if __selected_taxonomy__ == nil {
var err error
__selected_taxonomy__, err = ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
!CLIAreAlternativeNamesSelected())
if err != nil {
return nil, err
}
}
return __selected_taxonomy__, nil
}
return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
}
func OptionSet(options *getoptions.GetOpt) {
LoadTaxonomyOptionSet(options, true, true)
obioptions.LoadTaxonomyOptionSet(options, true, true)
FilterTaxonomyOptionSet(options)
options.BoolVar(&__fixed_pattern__, "fixed", false,
options.Alias("F"),